FMO DATABASE

FMODB ID: 1NRVZ

Calculation Name: 2RF4-F-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2RF4

Chain ID: F

ChEMBL ID:

UniProt ID: P50106

Base Structure: X-ray

Registration Date: 2023-09-24

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	60
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-284746.142813
FMO2-HF: Nuclear repulsion	261317.989146
FMO2-HF: Total energy	-23428.153667
FMO2-MP2: Total energy	-23498.141757

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(F:17:ASN)

Summations of interaction energy for fragment #1(F:17:ASN)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
0.284	2.259	-0.011	-0.851	-1.112	0.003

Interaction energy analysis for fragmet #1(F:17:ASN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.018 / q_NPA : -0.007

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

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Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	F	19	PRO	0	-0.025	0.013	3.819	-0.023	1.952	-0.011	-0.851	-1.112	0.003
4	F	20	VAL	0	0.037	0.010	5.611	0.286	0.286	0.000	0.000	0.000	0.000
5	F	21	VAL	0	-0.023	-0.014	8.736	0.371	0.371	0.000	0.000	0.000	0.000
6	F	22	ILE	0	-0.001	-0.007	11.844	0.019	0.019	0.000	0.000	0.000	0.000
7	F	23	HIS	0	0.008	0.005	14.664	0.114	0.114	0.000	0.000	0.000	0.000
8	F	24	ALA	0	-0.006	0.011	18.336	-0.007	-0.007	0.000	0.000	0.000	0.000
9	F	25	THR	0	0.016	-0.001	21.231	0.002	0.002	0.000	0.000	0.000	0.000
10	F	26	GLN	0	-0.034	-0.021	23.994	0.021	0.021	0.000	0.000	0.000	0.000
11	F	27	LEU	0	-0.005	0.009	25.009	0.003	0.003	0.000	0.000	0.000	0.000
12	F	28	PRO	0	-0.016	-0.030	23.723	-0.006	-0.006	0.000	0.000	0.000	0.000
13	F	29	GLN	0	0.024	0.031	26.314	0.008	0.008	0.000	0.000	0.000	0.000
14	F	30	HIS	0	-0.019	-0.010	28.423	0.002	0.002	0.000	0.000	0.000	0.000
15	F	31	VAL	0	0.011	0.007	28.561	-0.009	-0.009	0.000	0.000	0.000	0.000
16	F	32	SER	0	-0.039	-0.057	31.365	0.014	0.014	0.000	0.000	0.000	0.000
17	F	33	THR	0	0.040	-0.017	33.388	0.001	0.001	0.000	0.000	0.000	0.000
18	F	34	ASP	-1	-0.911	-0.965	34.728	-0.002	-0.002	0.000	0.000	0.000	0.000
19	F	35	GLU	-1	-0.826	-0.867	32.176	-0.024	-0.024	0.000	0.000	0.000	0.000
20	F	36	VAL	0	-0.030	-0.008	28.385	-0.009	-0.009	0.000	0.000	0.000	0.000
21	F	37	LEU	0	-0.012	-0.010	30.400	-0.003	-0.003	0.000	0.000	0.000	0.000
22	F	38	GLN	0	-0.012	-0.002	32.945	-0.010	-0.010	0.000	0.000	0.000	0.000
23	F	39	PHE	0	-0.006	0.001	23.208	-0.008	-0.008	0.000	0.000	0.000	0.000
24	F	40	LEU	0	-0.010	-0.012	26.363	-0.007	-0.007	0.000	0.000	0.000	0.000
25	F	41	GLU	-1	-0.797	-0.853	28.676	-0.021	-0.021	0.000	0.000	0.000	0.000
26	F	42	SER	0	0.019	-0.002	29.334	-0.007	-0.007	0.000	0.000	0.000	0.000
27	F	43	PHE	0	-0.023	-0.006	20.192	-0.016	-0.016	0.000	0.000	0.000	0.000
28	F	44	ILE	0	-0.045	-0.041	25.220	-0.005	-0.005	0.000	0.000	0.000	0.000
29	F	45	ASP	-1	-0.938	-0.954	27.026	-0.088	-0.088	0.000	0.000	0.000	0.000
30	F	46	GLU	-1	-0.850	-0.913	24.569	-0.202	-0.202	0.000	0.000	0.000	0.000
31	F	47	LYS	1	0.749	0.855	20.515	0.173	0.173	0.000	0.000	0.000	0.000
32	F	48	GLU	-1	-0.840	-0.889	24.359	-0.017	-0.017	0.000	0.000	0.000	0.000
33	F	49	ASN	0	-0.004	0.012	26.837	0.013	0.013	0.000	0.000	0.000	0.000
34	F	50	ILE	0	-0.014	-0.015	26.822	-0.009	-0.009	0.000	0.000	0.000	0.000
35	F	51	ILE	0	-0.089	-0.046	24.888	-0.013	-0.013	0.000	0.000	0.000	0.000
36	F	52	ASP	-1	-0.857	-0.935	24.041	-0.143	-0.143	0.000	0.000	0.000	0.000
37	F	78	ILE	0	-0.073	-0.030	16.558	-0.041	-0.041	0.000	0.000	0.000	0.000
38	F	79	ASP	-1	-0.811	-0.893	20.504	-0.088	-0.088	0.000	0.000	0.000	0.000
39	F	80	THR	0	0.029	0.005	14.512	0.002	0.002	0.000	0.000	0.000	0.000
40	F	81	ASN	0	-0.069	-0.035	16.145	0.038	0.038	0.000	0.000	0.000	0.000
41	F	82	LEU	0	0.029	0.016	17.392	0.050	0.050	0.000	0.000	0.000	0.000
42	F	83	SER	0	0.061	0.024	19.440	0.011	0.011	0.000	0.000	0.000	0.000
43	F	84	SER	0	-0.032	-0.012	20.930	-0.002	-0.002	0.000	0.000	0.000	0.000
44	F	85	SER	0	-0.008	-0.008	19.009	0.020	0.020	0.000	0.000	0.000	0.000
45	F	86	ILE	0	0.074	0.030	21.431	0.013	0.013	0.000	0.000	0.000	0.000
46	F	87	SER	0	-0.034	-0.007	24.163	0.002	0.002	0.000	0.000	0.000	0.000
47	F	88	GLN	0	-0.039	-0.029	22.740	0.011	0.011	0.000	0.000	0.000	0.000
48	F	89	LEU	0	0.050	0.022	22.480	0.005	0.005	0.000	0.000	0.000	0.000
49	F	90	LYS	1	0.806	0.886	26.248	-0.003	-0.003	0.000	0.000	0.000	0.000
50	F	91	ARG	1	0.863	0.933	28.615	-0.122	-0.122	0.000	0.000	0.000	0.000
51	F	92	ILE	0	0.024	0.020	25.473	0.002	0.002	0.000	0.000	0.000	0.000
52	F	93	GLN	0	0.005	-0.021	29.708	-0.006	-0.006	0.000	0.000	0.000	0.000
53	F	94	ARG	1	0.895	0.940	31.636	-0.081	-0.081	0.000	0.000	0.000	0.000
54	F	95	ASP	-1	-0.954	-0.964	32.815	0.098	0.098	0.000	0.000	0.000	0.000
55	F	96	PHE	0	0.054	-0.002	30.478	-0.003	-0.003	0.000	0.000	0.000	0.000
56	F	97	LYS	1	0.776	0.880	34.794	-0.011	-0.011	0.000	0.000	0.000	0.000
57	F	98	GLY	0	-0.039	-0.006	37.474	-0.004	-0.004	0.000	0.000	0.000	0.000
58	F	99	LEU	0	-0.021	-0.010	34.569	0.001	0.001	0.000	0.000	0.000	0.000
59	F	100	PRO	0	-0.039	0.000	38.959	-0.006	-0.006	0.000	0.000	0.000	0.000
60	F	101	PRO	0	-0.017	-0.002	41.756	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(F:17:ASN)